Purpose of this Page
This purpose of this page is to look at my annotated yeast gene, ADH1, and see how it's expression varies under different test conditions. DNA microarray data on ADH1 from various microarray databases will be displayed and discussed. This page serves as a guide which looks at a gene that has a know function and purpose. My other page "My Favorite Yeast Expression : YOL085C" will investigate a neighboring ORF of ADH1, YOL085C, that has no known function. The same analysis will be conducted on YOL085C as on ADH1. The goal of this section of my site is to find a function for the unannotated ORF YOL085C.
Databases Searched and Found Significant Results for ADH1
The microarray data for this figure does not yield much data for the repression of ADH1 at different alpha factor concentrations. All of the genes and ORFs that are clustered with ADH1 show no change in expression with the change in alpha factor concentrations, except SMT3, which implies that there is a glitch in the clustering algorithm that is used with this data analysis. Alpha factor is a pheromone used by alpha type yeast cells in their mating process. It makes sense that ADH1, which is involved in fermentation, would not be affected by changes in alpha factor.
See the Summary of the Gene Ontology annotations for this gene group
This data shows the expression of ADH1 in response to the presence of alpha factor. Like the previous data there is not much response in expression due to the presence of alpha factor. Likewise, the related genes and ORFs do not have significant changes in expression. Although there is a slight induction of all ORFs at the 120 minute mark. After two hours in the presence of alpha factor yeast cells are fairly far along in their reproductive cycle, at this point in the reproductive process there may be a function for ADH1 and related ORFs that are induced in this microarrray.
This test involves subjecting yeast cells to various types of damaging agents such as gamma radiation and heat. The only other gene compared to ADH1 is ADH2. Both proteins that are produced by ADH1 and ADH2 are intimately related in the fermentation process of yeast and it make sense that they are clustered together. The only significant response seen in the data is when the yeast cells are exposed to gamma radiation. When radiation is exposed to the mec1 mutant it ADH1 is represses and there is slight induction of ADH1 in wild type cells when irradiated. Mec1 is a gene involved in transcription of DNA; the affect that radiation has on ADH1 expression in a mec1 mutant confirms that repression of ADH1 and ADH2 hinders the fermentation process of yeast.
The trend of ADH1 expression shows a slight induction to slight repression during a diauxic shift in the environmental condition. The movement from a anaerobic to aerobic environment. has some influence on the expression of ADH1 which is reasonable because the fermentation process which ADH1 is involved in is a process that occurs in an anaerobic environment. The ORFs that are clustered with ADH1 also show a slight shift towards induction and then repression occurs at 20.5 hours. The ORFs that are clustered with ADH1 for this experiment are mainly involved in biosynthesis and transport of new cellular material. All of the processes of the genes clustered with ADH1 are directly related to energy supply that is available in yeast cells. The energy supply in yeast cells are partially governed by fermentation which ADH1 is involved in. Therefore the clustering of these cells in a microarray confirms that ADH1 is involved with the biosynthesis of a yeast cell.
There isn't a very significant change in the expression of ADH1 over three generations where a glucose supply is limited. There is slight repression in the first generation of yeast cells, which coincides with the diauxic shift results. The significant decrease in glucose will initially slow the fermentation process, just as a significant increase in oxygen repressed ADH1 in the diauxic shift experiment.
The microarray data for expression in response to environmental changes covers a variety of conditions. There is a definite ADH1 expression response to changes in temperature. ADH1 is proportionally induced to increases in temperature and proportionally repressed in temperature reduction. The presence of sorbitol in proximity to yeast does not change the expression of ADH1. However, oxydative stress caused by hydrogen peroxide and menadione caused drastic repression, especially with menadione, but after a period of time the expression of ADH1 in the presence of these oxydative agents returns to normal. It is worth noting that when the yeast is put through amino acid starvation ADH1 expression is repressed and after 2 hours ADH1 is induced to a equal degree. The other tests on ADH1 did not show any real significance on expression.
The ADH1 expression for the cell cycle analysis is uneventful for the majority of the cell cycle process. There are only two points of interest which are cdc15 at 230 minutes and cdc28 at 90 minutes. ADH1 is repressed to the same degree as HTA1 at cdc15 230 minutes, and the repression of ADH1 is inversely related to the induction of ASH1 and SWI5. Also, at cdc28 90 min it appears that ADH1 and ASH1 are induced equally while the other four reference genes have no change in expression. It is possible that at these two points ADH1 has a role in the yeast cell cycle and interacts with one or more of these reference genes. However, more investigation would need to be done to determine definitively that the ADH1 has a role in the cell cycle process. As mentioned previously the data indicates that ADH1 is not active other than the points cdc15 at 230 minutes and cdc28 at 90 minutes, and if ADH1 is involved in the cell cycle process it probably has a minor duty.
Sporulation is the process that involved yeast cells forming spores. This process appears to take place in aerobic conditions because the fermentation process appears to be severely repressed during sporulation. Oher synthesizing genes and transport genes are repressed, most likely because when sporulation occurs most of the biosynthetic processes that the gene above are associated with are a second priority during sporulation. I must conclude from this data that the energy that is required for sporulation takes place in aerobic conditions and derives its energy from a aerobic energy production source such as glycolysis.
This set of data is very revealing. The gene that regulates the zinc homeostasis of a cell is the Zap1 which encodes for the Zap1p transcription factor that regulates the transcription of Zrt1p,Zrt2p and Zrt3p transporter genes (Lyons, et al). As shown above, when there is extreme zinc deficiency there is a result of drastic induction of both ADH1 and ADH2 expression. This shows that ADH1 and ADH2, which are genes involved in fermentation, are also intimately involved in zinc homeostasis. From what is shown I infer that somehow zinc depletion is coupled with a anaerobic condition that induces fermentation. A zinc deficient condition may also hinder the aerobic energy production process and therefore require the use of fermentation for energy.
The microarray data that is collected on this page coincides with the function that ADH1 has in yeast cells. The most active behavior among the microarray data is in the sporulation and zinc depletion data. These two data sets had sudden drastic changes and fluctuations for ADH1 expression. One should be careful not to assume to much when interpreting this data because only a certain few genes are shown and the clustering algorithms that match other gene's expression to ADH1 are entirely artificial. Clustering among genes could be very different if a different clustering algorithm were used that could result in different correlations between genes observed that would lead to different interpretations of a gene's function.
Lyons TJ, et al. (2000) Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc Natl Acad Sci U S A 97(14):7957-62